5XSA | pdb_00005xsa

Crystal Structure of Transketolase in complex with TPP intermediate III from Pichia Stipitis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.97 Å
  • R-Value Free: 
    0.153 (Depositor), 0.153 (DCC) 
  • R-Value Work: 
    0.141 (Depositor), 0.141 (DCC) 
  • R-Value Observed: 
    0.142 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history

Literature

The Mesomeric Effect of Thiazolium on non-Kekule Diradicals in Pichia stipitis Transketolase.

Hsu, N.S.Wang, Y.L.Lin, K.H.Chang, C.F.Lyu, S.Y.Hsu, L.J.Liu, Y.C.Chang, C.Y.Wu, C.J.Li, T.L.

(2018) Angew Chem Int Ed Engl 57: 1802-1807

  • DOI: https://doi.org/10.1002/anie.201709799
  • Primary Citation Related Structures: 
    5XRY, 5XS6, 5XSA, 5XSB, 5XSM, 5XTL, 5XTV, 5XUF, 5XVT

  • PubMed Abstract: 

    It is theoretically plausible that thiazolium mesomerizes to congeners other than carbene in a low effective dielectric binding site; especially given the energetics and uneven electronegativity of carbene groups. However, such a phenomenon has never been reported. Nine crystal structures of transketolase obtained from Pichia stipitis (TKps) are reported with subatomic resolution, where thiazolium displays an extraordinary ring-bending effect. The bent thiazolium congeners correlate with non-Kekulé diradicals because there is no gain or loss of electrons. In conjunction with biophysical and biochemical analyses, it is concluded that ring bending is a result of tautomerization of thiazolium with its non- Kekulé diradicals, exclusively in the binding site of TKps. The chemophysical properties of these thiazolium mesomers may account for the great variety of reactivities carried out by thiamine-diphosphate-containing (ThDP) enzymes. The stability of ThDP in living systems can be regulated by the levels of substrates, and hydration and dehydration, as well as diradical-mediated oxidative degradation.


  • Organizational Affiliation
    • Genomics Research Center, Academia Sinica, Taipei, 115, Taiwan.

Macromolecule Content 

  • Total Structure Weight: 75.52 kDa 
  • Atom Count: 6,259 
  • Modeled Residue Count: 675 
  • Deposited Residue Count: 697 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Transketolase697Scheffersomyces stipitis CBS 6054Mutation(s): 0 
Gene Names: TKTTKT1PICST_67105
EC: 2.2.1.1
UniProt
Find proteins for P34736 (Scheffersomyces stipitis (strain ATCC 58785 / CBS 6054 / NBRC 10063 / NRRL Y-11545))
Explore P34736 
Go to UniProtKB:  P34736
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP34736
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
8EL
(Subject of Investigation/LOI)

Query on 8EL



Download:Ideal Coordinates CCD File
C [auth A]2-[3-[(4-azanyl-2-methyl-pyrimidin-5-yl)methyl]-4-methyl-2H-1,3-thiazol-5-yl]ethyl phosphono hydrogen phosphate
C12 H20 N4 O7 P2 S
FCUXBJDJFWOWMD-UHFFFAOYSA-N
CA
(Subject of Investigation/LOI)

Query on CA



Download:Ideal Coordinates CCD File
B [auth A]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.97 Å
  • R-Value Free:  0.153 (Depositor), 0.153 (DCC) 
  • R-Value Work:  0.141 (Depositor), 0.141 (DCC) 
  • R-Value Observed: 0.142 (Depositor) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 101.272α = 90
b = 185.469β = 90
c = 98.917γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
HKL-2000data collection

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-04-25
    Type: Initial release
  • Version 1.1: 2023-11-22
    Changes: Data collection, Database references, Derived calculations, Refinement description